Biochemistry
Biophysics Biophysics is the study of biomechanical systems through the lens of both biological and physical research. Modern biophysics is largely powered by technological advances from physics and engineering, allowing biological systems to be studied with precision and specficity never before imagined. Equilibrium Bio-Mechanics Biomechanics in systems in bio-equilibrium tend to be simpler and more consistent with time. Equilibrium bio-systems tend to have biodiverse populations of organisms of sustainable population sizes and live in environments that are predictable over fairly large timescales. More important to a species future, is its ability to adapt to the changing environments within its evolutionary time, changing breeding patterns in line with the seasons, setting hormonal clocks that are passed down epigenetically and bio-culturally to future generations to replicate the same cycles and remain in synchrony with the other species, this avoids any no long-term dominance of one species over others, which is covered in the field of 'non-equilibrium bio-mechanics'. Non-Equilibrium Bio-Mechanics Humans and Earth are part of a non-equilibrium bio-mechanical system. The Earth has been in constant flux for millennia and humans have thrived due to our development of domestication techniques of both animals and plants to out-plan the seasonal and cosmic fluctuations that terrorised our prior societies. Since the agricultural revolution during the Age of Taurus humans have broken out of the equilibrium phase of our evolution and learned to thrive under the non-equilibrium dynamics of a fertile planet with abundant food and energy, learning to expand our societies and develop new technologies to improve global productivity. However, with increased productivity and expanding society, comes war. The Age of Aries (aka the age of empires) is defined by the dominance of humans over animals, man over woman and indo-european society over the indigenous world. Mathematical Biophysics :"The Lotka–Volterra equations, also known as the predator–prey equations, are a pair of first-order nonlinear differential equations, frequently used to describe the dynamics of biological systems in which two species interact, one as a predator and the other as prey. The populations change through time according to the pair of equations: : \begin{align} \frac{dx}{dt} &= \alpha x - \beta x y, \\ \frac{dy}{dt} &= \delta x y - \gamma y, \end{align} :where :x is the number of prey (for example, rabbits); :y is the number of some predator (for example, foxes); : \tfrac{dy}{dt} and \tfrac{dx}{dt} represent the instantaneous growth rates of the two populations; :t represents time; : α, β, γ, δ are positive real parameters describing the interaction of the two species." (Also used to describe kinetics in the operation of Masers: 'microwave lasers') Biochemistry Bioinformatics 'Quantum DNA' * The Shannon Entropy of DNA * and its potential for quantum coherence. () :"The Shannon entropy is a standard measure for the order state of symbol sequences, such as, for example, DNA sequences. In order to incorporate correlations between symbols, the entropy of n-mers (consecutive strands of n symbols) has to be determined. Here, an assay is presented to estimate such higher order entropies (block entropies) for DNA sequences when the actual number of observations is small compared with the number of possible outcomes." :"Presumably, you have a motif (pattern) in a position weight matrix format? The motif has it's own entropy, regardless of any genome; it's just a measure of how much information is encoded in a motif." :"Thanks to advice and code from here and the theory and formula from here: H_i = - \sum f_{a,i} \times \log_2 f_{a,i} , :where f_{a,i} is the relative frequency of base or amino acid a at position i :I've adapted a Python script to answer my own question, hope this helps others in future: SHOWN" Exons & Introns :"The intron has been a big biological mystery since it was first discovered in several aspects. First, all of the completely sequenced eukaryotes harbor introns in the genomic structure, whereas no prokaryotes identified so far carry introns. Second, the amount of total introns varies in different species. Third, the length and number of introns vary in different genes, even within the same species genome. Fourth, all introns are copied into RNAs by transcription and DNAs by replication processes, but intron sequences do not participate in protein-coding sequences." :"This question relates to a curious feature of how genetic information is organized in the DNA of many organisms. The sequence of bases that make up DNA encode a corresponding sequence of amino acids which make up proteins. Molecular biologists had at first assumed that in a gene, all the DNA coding for a protein would be continuous, and that is what they found when they first looked at the genes of prokaryotes (bacteria and other simple cells). When researchers looked at more complex (eukaryotic) cells, however, they found that the encoding DNA is typically discontinuous: stretches of encoding DNA (called exons) are interspersed with long stretches of non-encoding DNA (called introns). After the DNA is transcribed into a string of RNA--but before the RNA is translated into protein--the introns are edited out. Although introns have sometimes been loosely called "junk DNA," the fact that they are so common and have been preserved during evolution leads many researchers to believe that they serve some function." :""First, let's start with some classifications. There are at least five different types of introns. Some of them are ribozymes, RNA molecules that are catalytically active, meaning that they facilitate certain chemical reactions; some of these ribozymes are able to perform a reaction in which they splice themselves out of the original transcript. The most common type of intron is called a spliceosomal or nuclear intron; the name comes from the cellular machinery, known as the spliceosome, which is responsible for splicing and making sure that the genetic sequences in introns are not translated into junk proteins. This type of intron is the one found in the nuclear genes of humans. :"In general, nuclear introns are widespread in complex eukaryotes, or higher organisms. Simple prokaryotes and eukaryotes (such as fungi and protozoa) lack them. In complex multicellular organisms (such as plants and vertebrates), introns are about 10-fold longer than the exons, the active, coding parts of the genome. The sequence and length of introns vary rapidly over evolutionary time." maybe this could be used as a test for astronomy/astrology? Introns may align with periods in evolutionary time which corresponds to specific 'dark periods' in earth's astronomical timeline. :""In 1978 Walter Gilbert of Harvard expressed a different view of the nature of introns (in the same report in which he coined the terms 'exon' and 'intron'). He suggested that introns could speed up evolution by promoting genetic recombinations between exons. This process (which he called 'exon shuffling') would be directly associated with formation of new genes. Introns, from this perspective, have a profound purpose. They serve as hot spots for recombination in the formation of new combinations of exons. In other words, they are in our genes because they have been used during evolution as a faster pathway to assemble new genes. Over the past 10 years, the exon shuffling idea has been supported by data from various experimental approaches. :"Several genome projects will be concluded in the next decade. They are expected to yield a huge amount of information about intron sequences. The new data should solve most of our basic questions about the functions of introns." :"Motivation: Topological entropy has been one of the most difficult to implement of all the entropy-theoretic notions. This is primarily due to finite sample effects and high-dimensionality problems. In particular, topological entropy has been implemented in previous literature to conclude that entropy of exons is higher than of introns, thus implying that exons are more ‘random’ than introns." :"We define a new approximation to topological entropy free from the aforementioned difficulties. We compute its expected value and apply this definition to the intron and exon regions of the human genome to observe that as expected, the entropy of introns are significantly higher than that of exons." Brain Physics :"Between 14 and 19 resonance frequencies were identified for each subject in the frequency range 500 Hz to 7.5 kHz. The two lowest resonance frequencies were found to be on the average 972 (range 828-1164) and 1230 (range 981-1417) Hz. The relative damping coefficients of all resonances were found to be between 2.6 and 8.9%. Due to the relatively high damping coefficients, it is assumed that the resonance frequencies do not significantly affect bone conducted sound." ---- }} Category:Biochemistry Category:Biophysics Category:Biology Category:Science Category:Chemistry Category:Physics